Data for: Identifying genetically redundant accessions in the globally largest cassava collection

Carvajal-Yepes, M.; Ospina Colorado, J.A.; Aranzales Rondon, E.; Velez Tobon, M.L.; Correa Abondano, M.A.; Barbosa Torres, N.C.; Wenzl, P. (2025) Data for: Identifying genetically redundant accessions in the globally largest cassava collection. https://doi.org/10.7910/DVN/JWNYFA

A diverse panel of cultivated cassava landraces and improved lines were genotyped using DArTSeq Technology to identify genetic redundancy within the genebank collection.

Methodology: Leaf samples were collected from in vitro plants for DNA extraction. The extracted DNA samples were subsequently sent to DArT P/L and genotyped using the DArTseq platform and sequencing, resulting in approximately 2.5 million reads per sample. Libraries were generated using the PstI and MseI restriction enzymes. To call SNPs and SilicoDArT genomic variants, the DS14 software was implemented. Genomic variants were reported in .csv files. SilicoDArT Format: SilicoDArTs are scored in a binary fashion, representing genetically 'dominant' markers, with '1' indicating the presence and '0' indicating the absence of a restriction fragment with the marker sequence in the genomic representation of the sample. 'NA' is used for missing data. SNP Format: '0' represents a reference allele homozygote, '2' represents an SNP allele homozygote, '1' represents a heterozygote, and 'NA' represents a double null/null allele homozygote (absence of a fragment with SNP in the genomic representation)